Experienced hooker Hartley has not played in nearly four weeks due to a knee injury and head coach Eddie Jones has revealed the 32-year-old will not feature against Joe Schmidt's men at the Aviva Stadium in Dublin.
"Dylan won't be available for the Ireland game so we won't take him to Portugal but we are hopeful he will be back later in the Championship," he was quoted as saying by BBC Sport.
"Owen will be captain by himself and he will certainly have great support from a number of senior players."
Scrum-half Danny Care, who recently expressed his desire to battle for a place in Jones' plans, has been left out of the 35-man squad, leaving Ben Youngs and Dan Robson, who is one of four uncapped players in the squad, to battle for the starting spot.
Forwards Ben Earl and Jack Singleton and centre Ollie Thorley, who can also provide cover on the wings, are the other three uncapped players hoping to make their debuts against Ireland. Prop Dan Cole and the Vunipola brothers, Mako and Billy, have all earned recalls but there is no place for flanker Chris Robshaw and centre Jonathan Joseph, who have not been considered because of injury.
England squad to face Ireland: Forwards: Jack Clifford, Dan Cole, Luke Cowan-Dickie, Tom Curry, Ben Earl, Ellis Genge, Jamie George, Nathan Hughes, Maro Itoje, George Kruis, Joe Launchbury, Courtney Lawes, Ben Moon, Brad Shields, Kyle Sinckler, Jack Singleton, Billy Vunipola, Mako Vunipola, Harry Williams, Mark Wilson. Backs: Chris Ashton, Mike Brown, Joe Cokanasiga, Elliot Daly, Ollie Devoto, Owen Farrell, George Ford, Jonny May, Jack Nowell, Dan Robson, Henry Slade, Ben Te'o, Ollie Thorley, Manu Tuilagi, Ben Youngs.